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custom-fileis pointing to an existent file with acustom-set-variableslist that contains the expected'(web-mode-script-padding 0)custom-fileactually loaded - do you load it in your init file, for example? If so, does something else later change the value? You can perhaps bisect your init file to find out the latter (usecomment-regionfor that).custom-filegets loaded by looking at the value of its options or faces. The init-file bisecting is to help you narrow down to the part of the file that causes the problem. Presumably, it's somewhere in the part after your init file loads yourcustom-file.